[2024-01-25 18:42:20,385] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference
[2024-01-25 18:42:21,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,529] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,529] [INFO] Running command: gunzip -c /var/lib/cwl/stgea0646be-0cb5-4236-8bdc-a8faa9d93fb6/GCF_002014855.1_ASM201485v1_genomic.fna.gz | prodigal -d GCF_002014855.1_ASM201485v1_genomic.fna/cds.fna -a GCF_002014855.1_ASM201485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:27,092] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:27,092] [INFO] Task started: HMMsearch
[2024-01-25 18:42:27,092] [INFO] Running command: hmmsearch --tblout GCF_002014855.1_ASM201485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/reference_markers.hmm GCF_002014855.1_ASM201485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:27,272] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:27,273] [INFO] Found 6/6 markers.
[2024-01-25 18:42:27,297] [INFO] Query marker FASTA was written to GCF_002014855.1_ASM201485v1_genomic.fna/markers.fasta
[2024-01-25 18:42:27,298] [INFO] Task started: Blastn
[2024-01-25 18:42:27,298] [INFO] Running command: blastn -query GCF_002014855.1_ASM201485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/reference_markers.fasta -out GCF_002014855.1_ASM201485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:27,922] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:27,926] [INFO] Selected 16 target genomes.
[2024-01-25 18:42:27,926] [INFO] Target genome list was writen to GCF_002014855.1_ASM201485v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:27,935] [INFO] Task started: fastANI
[2024-01-25 18:42:27,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0646be-0cb5-4236-8bdc-a8faa9d93fb6/GCF_002014855.1_ASM201485v1_genomic.fna.gz --refList GCF_002014855.1_ASM201485v1_genomic.fna/target_genomes.txt --output GCF_002014855.1_ASM201485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:34,262] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:34,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:34,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:34,272] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:34,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:34,273] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	100.0	715	715	95	conclusive
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	86.1121	488	715	95	below_threshold
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	79.2529	286	715	95	below_threshold
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	79.2101	291	715	95	below_threshold
Moraxella cuniculi	strain=NCTC10297	GCA_900637105.1	34061	34061	type	True	79.1063	290	715	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	79.0814	353	715	95	below_threshold
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	78.4619	201	715	95	below_threshold
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	78.4468	232	715	95	below_threshold
Moraxella ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	78.3921	199	715	95	below_threshold
Moraxella catarrhalis	strain=NCTC11020	GCA_900476075.1	480	480	type	True	78.3839	240	715	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	78.3042	193	715	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	76.8922	70	715	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	76.69	94	715	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	76.6281	78	715	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.4074	97	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:34,275] [INFO] DFAST Taxonomy check result was written to GCF_002014855.1_ASM201485v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:34,275] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:34,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:34,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/checkm_data
[2024-01-25 18:42:34,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:34,304] [INFO] Task started: CheckM
[2024-01-25 18:42:34,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014855.1_ASM201485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014855.1_ASM201485v1_genomic.fna/checkm_input GCF_002014855.1_ASM201485v1_genomic.fna/checkm_result
[2024-01-25 18:42:56,159] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:56,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:56,207] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:56,207] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:56,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014855.1_ASM201485v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:56,207] [INFO] Task started: Blastn
[2024-01-25 18:42:56,207] [INFO] Running command: blastn -query GCF_002014855.1_ASM201485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83e69da-1bdf-42a6-801f-f2b2ab888965/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014855.1_ASM201485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:57,265] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:57,268] [INFO] Selected 9 target genomes.
[2024-01-25 18:42:57,268] [INFO] Target genome list was writen to GCF_002014855.1_ASM201485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:57,275] [INFO] Task started: fastANI
[2024-01-25 18:42:57,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0646be-0cb5-4236-8bdc-a8faa9d93fb6/GCF_002014855.1_ASM201485v1_genomic.fna.gz --refList GCF_002014855.1_ASM201485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014855.1_ASM201485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:01,130] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:01,136] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:01,136] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002014855.1	s__Moraxella porci	100.0	715	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	conclusive
GCF_002014825.1	s__Moraxella pluranimalium	86.1079	488	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156515.1	s__Moraxella cuniculi	79.2539	286	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_002014965.1	s__Moraxella canis	79.0888	353	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_001656295.1	s__Moraxella catarrhalis_C	78.6517	315	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_001632285.1	s__Moraxella catarrhalis	78.4627	233	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_001636015.1	s__Moraxella ovis	78.3921	199	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
GCF_000696305.2	s__Moraxella bovoculi	78.3248	192	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:01,137] [INFO] GTDB search result was written to GCF_002014855.1_ASM201485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:01,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:01,140] [INFO] DFAST_QC result json was written to GCF_002014855.1_ASM201485v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:01,141] [INFO] DFAST_QC completed!
[2024-01-25 18:43:01,141] [INFO] Total running time: 0h0m41s